3-29341050-C-T

Variant names:

• chr3-29341050-C-T
• rs7431530
• NM_001003793.3:c.75+59294C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001003793.3(RBMS3):​c.75+59294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,698 control chromosomes in the GnomAD database, including 6,873 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (6873 hom., cov: 32)
• Consequence: RBMS3 NM_001003793.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 4 publications found

Genes affected

RBMS3 (HGNC:13427): (RNA binding motif single stranded interacting protein 3) This gene encodes an RNA-binding protein that belongs to the c-myc gene single-strand binding protein family. These proteins are characterized by the presence of two sets of ribonucleoprotein consensus sequence (RNP-CS) that contain conserved motifs, RNP1 and RNP2, originally described in RNA binding proteins, and required for DNA binding. These proteins have been implicated in such diverse functions as DNA replication, gene transcription, cell cycle progression and apoptosis. The encoded protein was isolated by virtue of its binding to an upstream element of the alpha2(I) collagen promoter. The observation that this protein localizes mostly in the cytoplasm suggests that it may be involved in a cytoplasmic function such as controlling RNA metabolism, rather than transcription. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]

ENSG00000283563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBMS3	NM_001003793.3	c.75+59294C>T		intron_variant	Intron 1 of 14	ENST00000383767.7	NP_001003793.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBMS3	ENST00000383767.7	c.75+59294C>T		intron_variant	Intron 1 of 14	1	NM_001003793.3	ENSP00000373277.2
ENSG00000283563	ENST00000635992.1	n.*583-93693C>T		intron_variant	Intron 8 of 13	5		ENSP00000489994.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45189 AN: 151578 Hom.: 6864 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.302

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.298 AC: 45243 AN: 151698 Hom.: 6873 Cov.: 32 AF XY: 0.297 AC XY: 22043 AN XY: 74126

African (AFR) AF: 0.349 AC: 14442 AN: 41360

American (AMR) AF: 0.340 AC: 5181 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3462

East Asian (EAS) AF: 0.352 AC: 1809 AN: 5142

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4804

European-Finnish (FIN) AF: 0.256 AC: 2691 AN: 10498

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18095 AN: 67906

Other (OTH) AF: 0.305 AC: 642 AN: 2108

Alfa AF: 0.265 Hom.: 8510

Bravo AF: 0.310

Asia WGS AF: 0.268 AC: 926 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.39
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7431530; hg19: chr3-29382541;